Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1735/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: devel
git_last_commit: d9a274e
git_last_commit_date: 2025-04-15 11:49:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on taishan

To the developers/maintainers of the ReactomeGSA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ReactomeGSA
Version: 1.23.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
StartedAt: 2025-10-17 12:39:21 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 12:58:00 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 1118.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReactomeGSA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_correlations,ReactomeAnalysisResult: no visible binding for global
  variable ‘combined_sig’
plot_correlations,ReactomeAnalysisResult: no visible binding for global
  variable ‘alpha’
plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
  variable ‘cluster_id’
plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
  variable ‘expr’
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable ‘gsva_result’
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable ‘PC1’
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable ‘PC2’
plot_heatmap,ReactomeAnalysisResult: no visible global function
  definition for ‘desc’
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable ‘n_sig’
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable ‘dataset’
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable ‘Name’
plot_volcano,ReactomeAnalysisResult: no visible binding for global
  variable ‘av_foldchange’
plot_volcano,ReactomeAnalysisResult: no visible binding for global
  variable ‘FDR’
Undefined global functions or variables:
  FDR Name PC1 PC2 alpha av_foldchange cluster_id combined_sig dataset
  desc expr gsva_result n_sig
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_heatmap-ReactomeAnalysisResult-method 55.041  2.156 100.783
plot_gsva_pca                                   53.416  0.981 100.246
plot_gsva_pathway-ReactomeAnalysisResult-method 53.175  0.810 101.348
plot_gsva_pca-ReactomeAnalysisResult-method     52.900  0.477  91.616
analyse_sc_clusters                             51.872  0.518  91.257
plot_gsva_pathway                               50.969  0.588  95.939
plot_gsva_heatmap                               50.220  0.874  94.902
analyse_sc_clusters-Seurat-method               49.644  1.194  94.461
analyse_sc_clusters-SingleCellExperiment-method 46.982  0.987 110.298
generate_pseudo_bulk_data                       17.460  0.690  18.261
ReactomeAnalysisRequest                          6.752  0.243   7.023
perform_reactome_analysis                        4.376  0.347  68.794
load_public_dataset                              1.717  0.095  36.152
find_public_datasets                             0.158  0.008   7.319
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘ReactomeGSA’ ...
** this is package ‘ReactomeGSA’ version ‘1.23.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘analyse_sc_clusters’ with signature ‘object="Seurat"’: no definition for class “Seurat”
in method for ‘analyse_sc_clusters’ with signature ‘object="SingleCellExperiment"’: no definition for class “SingleCellExperiment”
in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="EList"’: no definition for class “EList”
in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="DGEList"’: no definition for class “DGEList”
in method for ‘generate_pseudo_bulk_data’ with signature ‘object="Seurat"’: no definition for class “Seurat”
in method for ‘generate_pseudo_bulk_data’ with signature ‘object="SingleCellExperiment"’: no definition for class “SingleCellExperiment”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ReactomeGSA)

Tests output

ReactomeGSA.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ReactomeGSA)
> 
> test_check("ReactomeGSA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  2.412   0.172   2.579 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.7520.2437.023
ReactomeAnalysisResult-class0.2180.0040.225
add_dataset-ReactomeAnalysisRequest-DGEList-method1.1850.0321.220
add_dataset-ReactomeAnalysisRequest-EList-method0.8540.0120.868
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.8380.0040.844
add_dataset-ReactomeAnalysisRequest-data.frame-method0.8430.0160.861
add_dataset-ReactomeAnalysisRequest-matrix-method0.8520.0000.854
add_dataset0.8320.0000.834
analyse_sc_clusters-Seurat-method49.644 1.19494.461
analyse_sc_clusters-SingleCellExperiment-method 46.982 0.987110.298
analyse_sc_clusters51.872 0.51891.257
find_public_datasets0.1580.0087.319
generate_metadata0.0010.0000.001
generate_pseudo_bulk_data17.460 0.69018.261
get_public_species0.0500.0040.927
get_reactome_data_types0.0960.0082.621
get_reactome_methods0.1630.0083.029
get_result-ReactomeAnalysisResult-method0.5370.0430.610
get_result0.2580.0040.262
load_public_dataset 1.717 0.09536.152
names-ReactomeAnalysisResult-method0.2610.0000.287
open_reactome-ReactomeAnalysisResult-method0.2490.0080.259
open_reactome0.2550.0080.263
pathways-ReactomeAnalysisResult-method0.3250.0080.334
pathways0.270.000.27
perform_reactome_analysis 4.376 0.34768.794
plot_correlations-ReactomeAnalysisResult-method0.3800.0120.393
plot_correlations0.3320.0120.345
plot_gsva_heatmap-ReactomeAnalysisResult-method 55.041 2.156100.783
plot_gsva_heatmap50.220 0.87494.902
plot_gsva_pathway-ReactomeAnalysisResult-method 53.175 0.810101.348
plot_gsva_pathway50.969 0.58895.939
plot_gsva_pca-ReactomeAnalysisResult-method52.900 0.47791.616
plot_gsva_pca 53.416 0.981100.246
plot_heatmap-ReactomeAnalysisResult-method0.7100.0200.733
plot_heatmap0.8890.0040.896
plot_volcano-ReactomeAnalysisResult-method0.2810.0040.285
plot_volcano0.3000.0000.301
print-ReactomeAnalysisRequest-method0.0010.0000.001
print-ReactomeAnalysisResult-method0.2510.0040.256
reactome_links-ReactomeAnalysisResult-method0.2590.0080.268
reactome_links0.2610.0040.266
result_types-ReactomeAnalysisResult-method0.2580.0000.259
result_types0.2430.0090.253
set_method-ReactomeAnalysisRequest-method0.0020.0000.002
set_method0.0020.0000.002
set_parameters-ReactomeAnalysisRequest-method0.0020.0000.002
set_parameters0.0020.0000.001
show-ReactomeAnalysisRequest-method0.0010.0000.001
show-ReactomeAnalysisResult-method0.2450.0040.250